Fig. 4: Evolutionary divergence of local spatial context in ATs across seven mammalian species.

a Divergence times (million years ago, MYA) and phylogenetic tree topology of seven representative mammalian species retrieved from the TimeTree database (http://www.timetree.org/). The number in the parentheses indicates the range of divergence times. b Plot of Spearman’s r values showing the relationship (r = –0.481) between gene expression levels of 1-1 orthologs (n = 8020) and the divergence time for each pair of mammalian species. The statistical significance of the two-sided p value was calculated using hypothesis testing. c Plot of Spearman’s r values showing the relationship (r = –0.564) between the IS index of all bins (94,994 10-kb bins) and the divergence time for each pair of mammalian species. The statistical significance of the two-sided p value was calculated using hypothesis testing. Evolutionary distance is positively correlated with divergence in gene expression levels and with IS divergence across species. d Distribution pattern of IS levels, A/B compartment status, and Alu element for non-conserved states (state 21–26, see Supplementary Fig. 34 for details). Note the enrichment for SINE-Alu elements in human-specific high IS state 24. e Circular plot illustrating the overlap/intersection of transcription factor motifs enriched across non-conserved states. The six tracks in the middle represent the six states, with individual blocks showing the “presence” (colored) or “absence” (white) of the state in each intersection. The height of the bars in the outer layer is proportional to the intersection size. Numbers above each bar indicate overlapping TFs for each state. The color intensity of the bars represents the significance of the intersections, as denoted by its p value (χ² test). f Enrichment of 14 TFs that were specifically enriched in state 24. The statistical significance of the p value was calculated using χ² testing. Source data for (b–f) are provided as a Source Data file.